HEADER TRANSFERASE 21-MAY-07 2Q0D TITLE TERMINAL URIDYLYL TRANSFERASE 4 FROM TRYPANOSOMA BRUCEI WITH BOUND ATP COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA URIDYLYL TRANSFERASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: RNA URIDYLYLTRANSFERASE 4; COMPND 5 EC: 2.7.7.52; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TRYPANOSOMA BRUCEI; SOURCE 3 ORGANISM_TAXID: 5691; SOURCE 4 GENE: TUT4; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS TUTASE, TRYPANOSOMA, NUCLEOTIDYLTRANSFERASE, UTP-BINDING, RNA- KEYWDS 2 EDITING, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR J.STAGNO,H.LUECKE REVDAT 5 30-AUG-23 2Q0D 1 REMARK SEQADV LINK REVDAT 4 18-OCT-17 2Q0D 1 REMARK REVDAT 3 24-FEB-09 2Q0D 1 VERSN REVDAT 2 09-OCT-07 2Q0D 1 JRNL REVDAT 1 28-AUG-07 2Q0D 0 JRNL AUTH J.STAGNO,I.APHASIZHEVA,R.APHASIZHEV,H.LUECKE JRNL TITL DUAL ROLE OF THE RNA SUBSTRATE IN SELECTIVITY AND CATALYSIS JRNL TITL 2 BY TERMINAL URIDYLYL TRANSFERASES. JRNL REF PROC.NATL.ACAD.SCI.USA V. 104 14634 2007 JRNL REFN ISSN 0027-8424 JRNL PMID 17785418 JRNL DOI 10.1073/PNAS.0704259104 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.38 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 48158 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : TEST SET TAKEN FROM 2IKF REMARK 3 R VALUE (WORKING + TEST SET) : 0.222 REMARK 3 R VALUE (WORKING SET) : 0.221 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2473 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3236 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.50 REMARK 3 BIN R VALUE (WORKING SET) : 0.2850 REMARK 3 BIN FREE R VALUE SET COUNT : 179 REMARK 3 BIN FREE R VALUE : 0.3120 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5163 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 33 REMARK 3 SOLVENT ATOMS : 264 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.65 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.39000 REMARK 3 B22 (A**2) : -0.35000 REMARK 3 B33 (A**2) : -0.01000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.24000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.215 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.179 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.140 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.002 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.938 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.921 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5309 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7211 ; 1.547 ; 1.961 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 643 ; 6.179 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 252 ;35.690 ;23.294 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 890 ;17.878 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 46 ;18.428 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 809 ; 0.105 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4019 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2328 ; 0.204 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3558 ; 0.303 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 320 ; 0.162 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 69 ; 0.199 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 13 ; 0.277 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 3335 ; 0.940 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5226 ; 1.516 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2259 ; 2.120 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1985 ; 3.237 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 2Q0D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-MAY-07. REMARK 100 THE DEPOSITION ID IS D_1000042990. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-JUL-06 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK REMARK 200 DATA SCALING SOFTWARE : D*TREK 9.2L REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 48171 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 42.870 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 3.560 REMARK 200 R MERGE (I) : 0.09200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.27 REMARK 200 R MERGE FOR SHELL (I) : 0.46300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CCP4 SUITE REMARK 200 STARTING MODEL: PDB ENTRY 2IKF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM SODIUM CACODYLATE, 200 MM REMARK 280 CALCIUM ACETATE, 18% PEG-8000, 4 MM MGCL2, 50 UM ATP, PH 6.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 20.98500 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLY A -7 REMARK 465 LEU A -6 REMARK 465 VAL A -5 REMARK 465 PRO A -4 REMARK 465 ARG A -3 REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 PRO A 2 REMARK 465 LYS A 22 REMARK 465 ASP A 23 REMARK 465 LEU A 24 REMARK 465 HIS A 25 REMARK 465 THR A 26 REMARK 465 ARG A 27 REMARK 465 MET B -19 REMARK 465 GLY B -18 REMARK 465 SER B -17 REMARK 465 SER B -16 REMARK 465 HIS B -15 REMARK 465 HIS B -14 REMARK 465 HIS B -13 REMARK 465 HIS B -12 REMARK 465 HIS B -11 REMARK 465 HIS B -10 REMARK 465 SER B -9 REMARK 465 SER B -8 REMARK 465 GLY B -7 REMARK 465 LEU B -6 REMARK 465 VAL B -5 REMARK 465 PRO B -4 REMARK 465 ARG B -3 REMARK 465 GLY B -2 REMARK 465 SER B -1 REMARK 465 HIS B 0 REMARK 465 MET B 1 REMARK 465 PRO B 2 REMARK 465 PRO B 45 REMARK 465 LEU B 46 REMARK 465 MET B 47 REMARK 465 ARG B 118 REMARK 465 ARG B 119 REMARK 465 THR B 120 REMARK 465 ARG B 121 REMARK 465 VAL B 122 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O LEU A 329 O HOH A 683 2.07 REMARK 500 O GLY A 64 O HOH A 667 2.15 REMARK 500 OE2 GLU A 115 O HOH A 691 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 NH2 ARG A 217 O HOH A 678 1545 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG B 146 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ASP B 253 CB - CG - OD1 ANGL. DEV. = 5.6 DEGREES REMARK 500 ARG B 263 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG B 263 NE - CZ - NH2 ANGL. DEV. = -4.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASP A 44 110.28 -162.46 REMARK 500 ASP A 66 -178.22 -67.88 REMARK 500 ALA A 86 55.24 -111.04 REMARK 500 ALA A 132 26.80 40.61 REMARK 500 ASN A 285 -0.11 67.26 REMARK 500 SER B 111 31.37 -92.81 REMARK 500 ASN B 158 72.71 -154.64 REMARK 500 TRP B 274 59.07 -102.24 REMARK 500 ALA B 328 65.54 39.58 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ARG A 119 THR A 120 -145.60 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 66 OD2 REMARK 620 2 ASP A 68 OD2 98.9 REMARK 620 3 ATP A 501 O1B 148.7 88.1 REMARK 620 4 ATP A 501 O3G 88.6 165.1 79.0 REMARK 620 5 ATP A 501 O1A 132.8 101.5 74.2 82.3 REMARK 620 6 HOH A 507 O 74.7 75.3 136.3 119.4 70.1 REMARK 620 7 HOH A 664 O 74.4 84.9 75.9 84.7 149.1 139.9 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ATP A 501 O1A REMARK 620 2 HOH A 507 O 69.7 REMARK 620 3 HOH A 515 O 86.4 141.7 REMARK 620 4 HOH A 615 O 107.8 76.5 140.9 REMARK 620 5 HOH A 636 O 75.9 118.3 82.0 67.4 REMARK 620 6 HOH A 665 O 84.4 82.3 65.5 149.6 143.0 REMARK 620 7 HOH A 670 O 147.9 136.7 77.7 71.3 74.4 113.0 REMARK 620 8 HOH A 671 O 152.8 83.3 114.8 67.1 121.8 89.1 58.0 REMARK 620 N 1 2 3 4 5 6 7 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ATP A 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2IKF RELATED DB: PDB REMARK 900 THE SAME PROTEIN WITH BOUND UTP SUBSTRATE. REMARK 900 RELATED ID: 2NOM RELATED DB: PDB REMARK 900 THE SAME PROTEIN WITH BOUND DUTP SUBSTRATE. REMARK 900 RELATED ID: 2Q0C RELATED DB: PDB REMARK 900 RELATED ID: 2Q0E RELATED DB: PDB REMARK 900 RELATED ID: 2Q0F RELATED DB: PDB REMARK 900 RELATED ID: 2Q0G RELATED DB: PDB DBREF 2Q0D A 1 333 UNP Q381M1 Q381M1_9TRYP 1 333 DBREF 2Q0D B 1 333 UNP Q381M1 Q381M1_9TRYP 1 333 SEQADV 2Q0D MET A -19 UNP Q381M1 CLONING ARTIFACT SEQADV 2Q0D GLY A -18 UNP Q381M1 CLONING ARTIFACT SEQADV 2Q0D SER A -17 UNP Q381M1 CLONING ARTIFACT SEQADV 2Q0D SER A -16 UNP Q381M1 CLONING ARTIFACT SEQADV 2Q0D HIS A -15 UNP Q381M1 EXPRESSION TAG SEQADV 2Q0D HIS A -14 UNP Q381M1 EXPRESSION TAG SEQADV 2Q0D HIS A -13 UNP Q381M1 EXPRESSION TAG SEQADV 2Q0D HIS A -12 UNP Q381M1 EXPRESSION TAG SEQADV 2Q0D HIS A -11 UNP Q381M1 EXPRESSION TAG SEQADV 2Q0D HIS A -10 UNP Q381M1 EXPRESSION TAG SEQADV 2Q0D SER A -9 UNP Q381M1 CLONING ARTIFACT SEQADV 2Q0D SER A -8 UNP Q381M1 CLONING ARTIFACT SEQADV 2Q0D GLY A -7 UNP Q381M1 CLONING ARTIFACT SEQADV 2Q0D LEU A -6 UNP Q381M1 CLONING ARTIFACT SEQADV 2Q0D VAL A -5 UNP Q381M1 CLONING ARTIFACT SEQADV 2Q0D PRO A -4 UNP Q381M1 CLONING ARTIFACT SEQADV 2Q0D ARG A -3 UNP Q381M1 CLONING ARTIFACT SEQADV 2Q0D GLY A -2 UNP Q381M1 CLONING ARTIFACT SEQADV 2Q0D SER A -1 UNP Q381M1 CLONING ARTIFACT SEQADV 2Q0D HIS A 0 UNP Q381M1 CLONING ARTIFACT SEQADV 2Q0D MET B -19 UNP Q381M1 CLONING ARTIFACT SEQADV 2Q0D GLY B -18 UNP Q381M1 CLONING ARTIFACT SEQADV 2Q0D SER B -17 UNP Q381M1 CLONING ARTIFACT SEQADV 2Q0D SER B -16 UNP Q381M1 CLONING ARTIFACT SEQADV 2Q0D HIS B -15 UNP Q381M1 EXPRESSION TAG SEQADV 2Q0D HIS B -14 UNP Q381M1 EXPRESSION TAG SEQADV 2Q0D HIS B -13 UNP Q381M1 EXPRESSION TAG SEQADV 2Q0D HIS B -12 UNP Q381M1 EXPRESSION TAG SEQADV 2Q0D HIS B -11 UNP Q381M1 EXPRESSION TAG SEQADV 2Q0D HIS B -10 UNP Q381M1 EXPRESSION TAG SEQADV 2Q0D SER B -9 UNP Q381M1 CLONING ARTIFACT SEQADV 2Q0D SER B -8 UNP Q381M1 CLONING ARTIFACT SEQADV 2Q0D GLY B -7 UNP Q381M1 CLONING ARTIFACT SEQADV 2Q0D LEU B -6 UNP Q381M1 CLONING ARTIFACT SEQADV 2Q0D VAL B -5 UNP Q381M1 CLONING ARTIFACT SEQADV 2Q0D PRO B -4 UNP Q381M1 CLONING ARTIFACT SEQADV 2Q0D ARG B -3 UNP Q381M1 CLONING ARTIFACT SEQADV 2Q0D GLY B -2 UNP Q381M1 CLONING ARTIFACT SEQADV 2Q0D SER B -1 UNP Q381M1 CLONING ARTIFACT SEQADV 2Q0D HIS B 0 UNP Q381M1 CLONING ARTIFACT SEQRES 1 A 353 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 353 LEU VAL PRO ARG GLY SER HIS MET PRO PRO SER PRO ALA SEQRES 3 A 353 VAL VAL GLY ARG SER LEU VAL ASN SER PHE LYS GLN PHE SEQRES 4 A 353 VAL SER LYS ASP LEU HIS THR ARG HIS VAL ASP ALA THR SEQRES 5 A 353 TYR ARG LEU VAL LEU ASP CYS VAL ALA ALA VAL ASP PRO SEQRES 6 A 353 LEU MET ARG LEU TYR THR PHE GLY SER THR VAL VAL TYR SEQRES 7 A 353 GLY VAL HIS GLU LYS GLY SER ASP VAL ASP PHE VAL VAL SEQRES 8 A 353 LEU ASN LYS THR ASP VAL GLU ASP GLY LYS GLY GLY ASP SEQRES 9 A 353 ALA ALA THR GLN VAL ALA LYS GLY LEU GLN ALA ASP ILE SEQRES 10 A 353 LEU ALA LYS LEU ALA ARG VAL ILE ARG GLN LYS HIS LEU SEQRES 11 A 353 SER TRP ASN VAL GLU GLU VAL ARG ARG THR ARG VAL PRO SEQRES 12 A 353 VAL VAL ARG VAL LYS GLY GLY GLY ALA VAL ASP PHE ASP SEQRES 13 A 353 ILE THR ALA TYR ARG ARG ASN GLY VAL ARG ASN SER ALA SEQRES 14 A 353 LEU LEU ARG ALA TYR PHE GLU GLN ASN PRO PRO CYS ARG SEQRES 15 A 353 TRP LEU SER MET SER ILE LYS ARG TRP SER LYS GLN THR SEQRES 16 A 353 GLY LEU ASN ALA SER VAL ILE GLY GLY SER ILE THR SER SEQRES 17 A 353 TYR GLY PHE ASN LEU MET VAL VAL TYR TYR LEU LEU GLN SEQRES 18 A 353 ARG ASN HIS LEU GLN PHE VAL PRO PRO SER THR ILE ASP SEQRES 19 A 353 VAL SER ARG VAL GLU PRO LEU PRO PRO HIS LEU PRO LEU SEQRES 20 A 353 GLU GLU PRO ALA ASP GLU GLY LEU GLU LEU GLY THR GLN SEQRES 21 A 353 VAL LEU ASP PHE LEU HIS PHE PHE LEU HIS GLU PHE ASP SEQRES 22 A 353 SER ASP LYS GLN VAL ILE SER LEU ASN ARG PRO GLY ILE SEQRES 23 A 353 THR THR LYS GLU GLU LEU ASP TRP THR LYS SER ALA GLU SEQRES 24 A 353 ASP PHE ALA ARG MET ASN GLY GLU LYS VAL HIS TYR GLN SEQRES 25 A 353 TRP CYS ILE GLU ASP PRO TYR GLU LEU ASN LEU ASN VAL SEQRES 26 A 353 GLY ARG ASN VAL THR PRO LEU LYS ARG ASP PHE LEU ARG SEQRES 27 A 353 ARG HIS LEU GLU LYS ALA ARG ASP THR ALA LEU LEU THR SEQRES 28 A 353 ILE VAL SEQRES 1 B 353 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 B 353 LEU VAL PRO ARG GLY SER HIS MET PRO PRO SER PRO ALA SEQRES 3 B 353 VAL VAL GLY ARG SER LEU VAL ASN SER PHE LYS GLN PHE SEQRES 4 B 353 VAL SER LYS ASP LEU HIS THR ARG HIS VAL ASP ALA THR SEQRES 5 B 353 TYR ARG LEU VAL LEU ASP CYS VAL ALA ALA VAL ASP PRO SEQRES 6 B 353 LEU MET ARG LEU TYR THR PHE GLY SER THR VAL VAL TYR SEQRES 7 B 353 GLY VAL HIS GLU LYS GLY SER ASP VAL ASP PHE VAL VAL SEQRES 8 B 353 LEU ASN LYS THR ASP VAL GLU ASP GLY LYS GLY GLY ASP SEQRES 9 B 353 ALA ALA THR GLN VAL ALA LYS GLY LEU GLN ALA ASP ILE SEQRES 10 B 353 LEU ALA LYS LEU ALA ARG VAL ILE ARG GLN LYS HIS LEU SEQRES 11 B 353 SER TRP ASN VAL GLU GLU VAL ARG ARG THR ARG VAL PRO SEQRES 12 B 353 VAL VAL ARG VAL LYS GLY GLY GLY ALA VAL ASP PHE ASP SEQRES 13 B 353 ILE THR ALA TYR ARG ARG ASN GLY VAL ARG ASN SER ALA SEQRES 14 B 353 LEU LEU ARG ALA TYR PHE GLU GLN ASN PRO PRO CYS ARG SEQRES 15 B 353 TRP LEU SER MET SER ILE LYS ARG TRP SER LYS GLN THR SEQRES 16 B 353 GLY LEU ASN ALA SER VAL ILE GLY GLY SER ILE THR SER SEQRES 17 B 353 TYR GLY PHE ASN LEU MET VAL VAL TYR TYR LEU LEU GLN SEQRES 18 B 353 ARG ASN HIS LEU GLN PHE VAL PRO PRO SER THR ILE ASP SEQRES 19 B 353 VAL SER ARG VAL GLU PRO LEU PRO PRO HIS LEU PRO LEU SEQRES 20 B 353 GLU GLU PRO ALA ASP GLU GLY LEU GLU LEU GLY THR GLN SEQRES 21 B 353 VAL LEU ASP PHE LEU HIS PHE PHE LEU HIS GLU PHE ASP SEQRES 22 B 353 SER ASP LYS GLN VAL ILE SER LEU ASN ARG PRO GLY ILE SEQRES 23 B 353 THR THR LYS GLU GLU LEU ASP TRP THR LYS SER ALA GLU SEQRES 24 B 353 ASP PHE ALA ARG MET ASN GLY GLU LYS VAL HIS TYR GLN SEQRES 25 B 353 TRP CYS ILE GLU ASP PRO TYR GLU LEU ASN LEU ASN VAL SEQRES 26 B 353 GLY ARG ASN VAL THR PRO LEU LYS ARG ASP PHE LEU ARG SEQRES 27 B 353 ARG HIS LEU GLU LYS ALA ARG ASP THR ALA LEU LEU THR SEQRES 28 B 353 ILE VAL HET MG A 401 1 HET MG A 402 1 HET ATP A 501 31 HETNAM MG MAGNESIUM ION HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE FORMUL 3 MG 2(MG 2+) FORMUL 5 ATP C10 H16 N5 O13 P3 FORMUL 6 HOH *264(H2 O) HELIX 1 1 SER A 4 PHE A 16 1 13 HELIX 2 2 PHE A 16 SER A 21 1 6 HELIX 3 3 VAL A 29 ASP A 44 1 16 HELIX 4 4 GLY A 53 GLY A 59 1 7 HELIX 5 5 ASN A 73 ASP A 79 1 7 HELIX 6 6 THR A 87 HIS A 109 1 23 HELIX 7 7 ARG A 142 ASN A 158 1 17 HELIX 8 8 CYS A 161 THR A 175 1 15 HELIX 9 9 THR A 187 ARG A 202 1 16 HELIX 10 10 PRO A 209 ILE A 213 5 5 HELIX 11 11 ASP A 214 VAL A 218 5 5 HELIX 12 12 GLY A 234 GLU A 251 1 18 HELIX 13 13 LYS A 269 ASP A 273 1 5 HELIX 14 14 THR A 275 ALA A 282 1 8 HELIX 15 15 THR A 310 ALA A 328 1 19 HELIX 16 16 SER B 4 PHE B 16 1 13 HELIX 17 17 PHE B 16 SER B 21 1 6 HELIX 18 18 THR B 26 VAL B 43 1 18 HELIX 19 19 GLY B 53 GLY B 59 1 7 HELIX 20 20 THR B 75 GLY B 80 1 6 HELIX 21 21 THR B 87 HIS B 109 1 23 HELIX 22 22 ARG B 142 ASN B 158 1 17 HELIX 23 23 CYS B 161 THR B 175 1 15 HELIX 24 24 THR B 187 ARG B 202 1 16 HELIX 25 25 PRO B 209 ILE B 213 5 5 HELIX 26 26 GLY B 234 GLU B 251 1 18 HELIX 27 27 LYS B 269 ASP B 273 1 5 HELIX 28 28 THR B 275 ASN B 285 1 11 HELIX 29 29 THR B 310 THR B 327 1 18 SHEET 1 A 5 ARG A 48 PHE A 52 0 SHEET 2 A 5 VAL A 67 LEU A 72 -1 O LEU A 72 N ARG A 48 SHEET 3 A 5 ASP A 134 ALA A 139 1 O ASP A 136 N PHE A 69 SHEET 4 A 5 VAL A 124 LYS A 128 -1 N VAL A 127 O PHE A 135 SHEET 5 A 5 ASN A 113 VAL A 117 -1 N GLU A 115 O ARG A 126 SHEET 1 B 2 GLN A 257 VAL A 258 0 SHEET 2 B 2 THR A 267 THR A 268 -1 O THR A 267 N VAL A 258 SHEET 1 C 2 ARG A 283 MET A 284 0 SHEET 2 C 2 GLU A 287 LYS A 288 -1 O GLU A 287 N MET A 284 SHEET 1 D 5 LEU B 49 PHE B 52 0 SHEET 2 D 5 VAL B 67 VAL B 71 -1 O ASP B 68 N PHE B 52 SHEET 3 D 5 PHE B 135 ALA B 139 1 O THR B 138 N VAL B 71 SHEET 4 D 5 VAL B 124 GLY B 129 -1 N VAL B 127 O PHE B 135 SHEET 5 D 5 TRP B 112 GLU B 116 -1 N ASN B 113 O LYS B 128 SHEET 1 E 2 GLN B 257 VAL B 258 0 SHEET 2 E 2 THR B 267 THR B 268 -1 O THR B 267 N VAL B 258 LINK OD2 ASP A 66 MG MG A 401 1555 1555 2.32 LINK OD2 ASP A 68 MG MG A 401 1555 1555 2.33 LINK MG MG A 401 O1B ATP A 501 1555 1555 2.38 LINK MG MG A 401 O3G ATP A 501 1555 1555 2.10 LINK MG MG A 401 O1A ATP A 501 1555 1555 2.63 LINK MG MG A 401 O HOH A 507 1555 1555 2.34 LINK MG MG A 401 O HOH A 664 1555 1555 2.53 LINK MG MG A 402 O1A ATP A 501 1555 1555 2.47 LINK MG MG A 402 O HOH A 507 1555 1555 2.55 LINK MG MG A 402 O HOH A 515 1555 1555 2.56 LINK MG MG A 402 O HOH A 615 1555 1555 2.74 LINK MG MG A 402 O HOH A 636 1555 1555 2.63 LINK MG MG A 402 O HOH A 665 1555 1555 2.34 LINK MG MG A 402 O HOH A 670 1555 1555 2.86 LINK MG MG A 402 O HOH A 671 1555 1555 2.43 SITE 1 AC1 5 ASP A 66 ASP A 68 ATP A 501 HOH A 507 SITE 2 AC1 5 HOH A 664 SITE 1 AC2 8 ATP A 501 HOH A 507 HOH A 515 HOH A 615 SITE 2 AC2 8 HOH A 636 HOH A 665 HOH A 670 HOH A 671 SITE 1 AC3 30 PHE A 52 GLY A 53 SER A 54 SER A 65 SITE 2 AC3 30 ASP A 66 ASP A 68 ARG A 121 GLY A 144 SITE 3 AC3 30 ASN A 147 SER A 148 LYS A 169 LYS A 173 SITE 4 AC3 30 THR A 187 SER A 188 TYR A 189 LEU A 303 SITE 5 AC3 30 VAL A 305 ARG A 307 MG A 401 MG A 402 SITE 6 AC3 30 HOH A 505 HOH A 507 HOH A 515 HOH A 548 SITE 7 AC3 30 HOH A 551 HOH A 556 HOH A 579 HOH A 636 SITE 8 AC3 30 HOH A 664 HOH A 672 CRYST1 80.190 41.970 106.420 90.00 94.01 90.00 P 1 21 1 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.012470 0.000000 0.000874 0.00000 SCALE2 0.000000 0.023827 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009420 0.00000